Differential methylation of genes and repeats in land plants

Rabinowicz, Pablo D.; Citek, Robert W.; Budiman, Muhammad A.; Nunberg, Andrew N.; Bedell, Joseph A.; Lakey, Nathan; O’Shaughnessy, Andrew; Nascimento, Lidia; McCombie, W. Richard; Martienssen, Robert A.

doi:10.1101/gr.4100405

Cited by 136 publications

(133 citation statements)

References 104 publications

(112 reference statements)

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“…The results indicate that Jinling elements are highly methylated at both of the CNG and CG sites (Figure 6). DNA methylation is often associated with reduced gene expression and previous studies in maize and Arabidopsis have also shown that repetitive sequences in heterochromatin are highly methylated (Bennetzen et al 1994;Lippman et al 2004;Rabinowicz et al 2005). A blastn search against .180,000 tomato ESTs (www.sgn.cornell.…”

Section: Resultsmentioning

confidence: 99%

Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome

Wang¹,

et al. 2006

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Eleven sequenced BACs were annotated and localized via FISH to tomato pachytene chromosomes providing the first global insights into the compositional differences of euchromatin and pericentromeric heterochromatin in this model dicot species. The results indicate that tomato euchromatin has a gene density (6.7 kb/gene) similar to that of Arabidopsis and rice. Thus, while the euchromatin comprises only 25% of the tomato nuclear DNA, it is sufficient to account for 90% of the estimated 38,000 nontransposon genes that compose the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10-100 times lower than that of the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin-the most abundant transposons belonging to the Jinling Ty3/gypsy -like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently-well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and on sequencing the genomes of tomato and other solanaceous species are discussed.

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Section: Resultsmentioning

confidence: 99%

Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome

Wang¹,

et al. 2006

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“…In higher plants, methylation of cytosines is present in CG, CHG (where H is A, C, or T), and asymmetric CHH sequence contexts (Henderson and Jacobsen, 2007). Recent studies have shown that cytosines are methylated not only in plant repetitive sequences and transposable elements (TEs) but also in promoters and gene bodies and that DNA methylation is highly correlated with transcription (Rabinowicz et al, 2005;Zhang et al, 2006;Vaughn et al, 2007;Zilberman et al, 2007;Cokus et al, 2008;Li et al, 2008c;Lister et al, 2008). Epigenetic changes, such as DNA methylation and histone modifications, do not act in isolation but rather in concert with each other, allowing for complex interdependencies.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

Elling

Wang²

2009

The Plant Cell

299

308

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Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organspecific distribution of canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), indicative of their tissue-specific biogenesis. Furthermore, we observed that a decreasing level of mop1 led to a concomitant decrease of 24-nucleotide siRNAs relative to 21-nucleotide miRNAs in a tissue-specific manner. A group of 22-nucleotide siRNAs may originate from long-hairpin double-stranded RNAs and preferentially target gene-coding regions. Additionally, a class of miRNA-like smRNAs, whose putative precursors can form short hairpins, potentially targets genes in trans. In summary, our data provide a critical analysis of the maize epigenome and its relationships to mRNA and smRNA transcriptomes.

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“…Examples for several genes related to fiber development are provided. Given that the total number of genes in the cotton genome may be 50,000 (Rabinowicz et al 2005), the 1484 gene pairs tested here include perhaps 5% of the total genic diversity. This suggests that for every 5 genes suggested as candidates for novel gene recruitment, another 95 exist that were not explored.…”

mentioning

confidence: 99%

Parallel Domestication, Convergent Evolution and Duplicated Gene Recruitment in Allopolyploid Cotton

Hovav¹,

Chaudhary²,

Udall³

et al. 2008

Genetics

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A putative advantage of allopolyploidy is the possibility of differential selection of duplicated (homeologous) genes originating from two different progenitor genomes. In this note we explore this hypothesis using a high throughput, SNP-specific microarray technology applied to seed trichomes (cotton) harvested from three developmental time points in wild and modern accessions of two independently domesticated cotton species, Gossypium hirsutum and G. barbadense. We show that homeolog expression ratios are dynamic both developmentally and over the several-thousand-year period encompassed by domestication and crop improvement, and that domestication increased the modulation of homeologous gene expression. In both species, D-genome expression was preferentially enhanced under human selection pressure, but for nonoverlapping sets of genes for the two independent domestication events. Our data suggest that human selection may have operated on different components of the fiber developmental genetic program in G. hirsutum and G. barbadense, leading to convergent rather than parallel genetic alterations and resulting morphology.

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Differential methylation of genes and repeats in land plants

Cited by 136 publications

References 104 publications

Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome

Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

Parallel Domestication, Convergent Evolution and Duplicated Gene Recruitment in Allopolyploid Cotton

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